Estimating DNA coverage and abundance in metagenomes using a gamma approximation

Motivation: Shotgun sequencing generates large numbers of short DNA reads from either an isolated organism or, in the case of metagenomics projects, from the aggregate genome of a microbial community. These reads are then assembled based on overlapping sequences into larger, contiguous sequences (contigs). The feasibility of assembly and the coverage achieved (reads per nucleotide or distinct sequence of nucleotides) depend on several factors: the number of reads sequenced, the read length and the relative abundances of their source genomes in the microbial community. A low coverage suggests that most of the genomic DNA in the sample has not been sequenced, but it is often difficult to estimate either the extent of the uncaptured diversity or the amount of additional sequencing that would be most efficacious. In this work, we regard a metagenome as a population of DNA fragments (bins), each of which may be covered by one or more reads. We employ a gamma distribution to model this bin population due to its flexibility and ease of use. When a gamma approximation can be found that adequately fits the data, we may estimate the number of bins that were not sequenced and that could potentially be revealed by additional sequencing. We evaluated the performance of this model using simulated metagenomes and demonstrate its applicability on three recent metagenomic datasets

Accurate Treatment of Large Supramolecular Complexes by Double-Hybrid Density Functionals Coupled with Nonlocal van der Waals Corrections

In this work, we present a thorough assessment of the performance of some representative double-hybrid density functionals (revPBE0-DH-NL and B2PLYP-NL) as well as their parent hybrid and GGA counterparts, in combination with the most modern version of the nonlocal (NL) van der Waals correction to describe very large weakly interacting molecular systems dominated by noncovalent interactions. Prior to the assessment, an accurate and homogeneous set of reference interaction energies was computed for the supramolecular complexes constituting the L7 and S12L data sets by using the novel, precise, and efficient DLPNO-CCSD(T) method at the complete basis set limit (CBS). The correction of the basis set superposition error and the inclusion of the deformation energies (for the S12L set) have been crucial for obtaining precise DLPNO-CCSD(T)/CBS interaction energies. Among the density functionals evaluated, the double-hybrid revPBE0-DH-NL and B2PLYP-NL with the three-body dispersion correction provide remarkably accurate association energies very close to the chemical accuracy. Overall, the NL van der Waals approach combined with proper density functionals can be seen as an accurate and affordable computational tool for the modeling of large weakly bonded supramolecular systems.Financial support by the “Ministerio de Economía y Competitividad” (MINECO) of Spain and European FEDER funds through projects CTQ2011-27253 and CTQ2012-31914 is acknowledged. The support of the Generalitat Valenciana (Prometeo/2012/053) is also acknowledged. J.A. thanks the EU for the FP7-PEOPLE-2012-IEF-329513 grant. J.C. acknowledges the “Ministerio de Educación, Cultura y Deporte” (MECD) of Spain for a predoctoral FPU grant

Systematic High-Accuracy Prediction of Electron Affinities for Biological Quinones

Quinones play vital roles as electron carriers in fundamental biological processes; therefore, the ability to accurately predict their electron affinities is crucial for understanding their properties and function. The increasing availability of cost‐effective implementations of correlated wave function methods for both closed‐shell and open‐shell systems offers an alternative to density functional theory approaches that have traditionally dominated the field despite their shortcomings. Here, we define a benchmark set of quinones with experimentally available electron affinities and evaluate a range of electronic structure methods, setting a target accuracy of 0.1 eV. Among wave function methods, we test various implementations of coupled cluster (CC) theory, including local pair natural orbital (LPNO) approaches to canonical and parameterized CCSD, the domain‐based DLPNO approximation, and the equations‐of‐motion approach for electron affinities, EA‐EOM‐CCSD. In addition, several variants of canonical, spin‐component‐scaled, orbital‐optimized, and explicitly correlated (F12) Møller–Plesset perturbation theory are benchmarked. Achieving systematically the target level of accuracy is challenging and a composite scheme that combines canonical CCSD(T) with large basis set LPNO‐based extrapolation of correlation energy proves to be the most accurate approach. Methods that offer comparable performance are the parameterized LPNO‐pCCSD, the DLPNO‐CCSD(T0), and the orbital optimized OO‐SCS‐MP2. Among DFT methods, viable practical alternatives are only the M06 and the double hybrids, but the latter should be employed with caution because of significant basis set sensitivity. A highly accurate yet cost‐effective DLPNO‐based coupled cluster approach is used to investigate the methoxy conformation effect on the electron affinities of ubiquinones found in photosynthetic bacterial reaction centers. © 2018 Wiley Periodicals, Inc

Le relatif succès d'une politique d'aménagement : J. Lieutaud, La Pouille, un exemple de programmation industrielle dans le Mezzogiorno italien

Vallat Colette. Le relatif succès d'une politique d'aménagement : J. Lieutaud, La Pouille, un exemple de programmation industrielle dans le Mezzogiorno italien. In: Annales de Géographie, t. 102, n°573, 1993. pp. 557-558

Quantum computing in pharma: A multilayer embedding approach for near future applications

Quantum computers are special purpose machines that are expected to be particularly useful in simulating strongly correlated chemical systems. The quantum computer excels at treating a moderate number of orbitals within an active space in a fully quantum mechanical manner. We present a quantum phase estimation calculation on F2 in a (2,2) active space on Rigetti's Aspen-11 QPU. While this is a promising start, it also underlines the need for carefully selecting the orbital spaces treated by the quantum computer. In this work, a scheme for selecting such an active space automatically is described and simulated results obtained using both the quantum phase estimation (QPE) and variational quantum eigensolver (VQE) algorithms are presented and combined with a subtractive method to enable accurate description of the environment. The active occupied space is selected from orbitals localized on the chemically relevant fragment of the molecule, while the corresponding virtual space is chosen based on the magnitude of interactions with the occupied space calculated from perturbation theory. This protocol is then applied to two chemical systems of pharmaceutical relevance: the enzyme [Fe] hydrogenase and the photosenzitizer temoporfin. While the sizes of the active spaces currently amenable to a quantum computational treatment are not enough to demonstrate quantum advantage, the procedure outlined here is applicable to any active space size, including those that are outside the reach of classical computation

New Boron(III) Blue Emitters for All-Solution Processed OLEDs: Molecular Design Assisted by Theoretical Modeling

Luminescent boron(III) complexes have recently been employed as emitters in organic light-emitting diodes (OLEDs) with reasonable success. They are easy to prepare and sufficiently stable to be used in such devices, being of great interest as a simple molecular emissive layer. Although emitters for this class with all colors have already been reported, highly efficient and stable blue emitters for applications in solution processed devices still pose a challenge. Here, we report the design, synthesis, and characterization of new boron complexes based on the 2-(benzothiazol-2-yl)phenol ligand (HBT), with different donor and acceptor groups responsible for modulating the emission properties, from blue to red. The molecular design was assisted by calculations using our newly developed formalism, where we demonstrate that the absorption and fluorescence spectra can be successfully predicted, which is a powerful technique to evaluate molecular photophysical properties prior to synthesis. In addition, density functional theory (DFT) enables us to understand the molecular and electronic structure of the molecules in greater detail. The molecules studied here presented fluorescence efficiencies as high as Φ = 0.88 and all solution processed OLEDs were prepared and characterized under an ambient atmosphere, after dispersion in the emitting layer. Surprisingly, even considering these rather simple experimental conditions, the blue emitters displayed superior properties compared to those in the present literature, in particular with respect to the stability of the current efficiency